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fix(loadImageData): Scale to Modality pixels or SUV when inserting sl…
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…ices into volume (0.0.12)
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@swederik
swederik committed Sep 1, 2019
1 parent 9254c8c commit ecae76f
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Showing 8 changed files with 254 additions and 149 deletions.
17 changes: 8 additions & 9 deletions example/package.json
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Original file line number Diff line number Diff line change
Expand Up @@ -15,12 +15,12 @@
"bfj": "6.1.1",
"case-sensitive-paths-webpack-plugin": "2.2.0",
"chalk": "2.4.2",
"cornerstone-core": "^2.2.8",
"cornerstone-tools": "3.11.0",
"cornerstone-wado-image-loader": "^2.2.3",
"cornerstone-core": "^2.3.0",
"cornerstone-tools": "3.19.1",
"cornerstone-wado-image-loader": "^3.0.0",
"css-loader": "2.1.1",
"dicom-parser": "^1.8.3",
"dicomweb-client": "^0.4.4",
"dicomweb-client": "^0.5.2",
"dotenv": "8.0.0",
"dotenv-expand": "5.1.0",
"eslint": "5.16.0",
Expand Down Expand Up @@ -49,7 +49,7 @@
"prop-types": "^15.7.2",
"react": "^16.8.6",
"react-app-polyfill": "^1.0.1",
"react-cornerstone-viewport": "0.1.29",
"react-cornerstone-viewport": "0.2.2",
"react-dev-utils": "^7.0.5",
"react-dom": "^16.8.6",
"react-resize-detector": "^4.1.3",
Expand All @@ -61,17 +61,16 @@
"style-loader": "0.23.1",
"terser-webpack-plugin": "1.2.4",
"url-loader": "1.1.2",
"vtk.js": "^8.13.0",
"vtk.js": "^11.0.1",
"webpack": "4.32.2",
"webpack-dev-server": "3.4.1",
"webpack-manifest-plugin": "2.0.4",
"workbox-webpack-plugin": "4.3.1"
},
"scripts": {
"version": "node -p -e \"'export default \\'' + require('./package.json').version + '\\';'\" > src/version.js",
"copy:webworkers": "cpx \"node_modules/cornerstone-wado-image-loader/dist/*.min.js*\" public",
"start": "yarn run copy:webworkers && node scripts/start.js",
"build": "yarn run copy:webworkers && node scripts/build.js",
"start": "node scripts/start.js",
"build": "node scripts/build.js",
"test": "node scripts/test.js --env=jsdom"
},
"jest": {
Expand Down
85 changes: 49 additions & 36 deletions example/src/VTKFusionExample.js
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,10 @@ import vtkColorMaps from 'vtk.js/Sources/Rendering/Core/ColorTransferFunction/Co

import presets from './presets.js'

window.cornerstoneWADOImageLoader = cornerstoneWADOImageLoader;

const url = 'https://server.dcmjs.org/dcm4chee-arc/aets/DCM4CHEE/rs'
//const url = 'http://localhost:8080/dcm4chee-arc/aets/DCM4CHEE/rs'
const client = new api.DICOMwebClient({ url })
const studyInstanceUID =
'1.3.6.1.4.1.14519.5.2.1.2744.7002.373729467545468642229382466905'
Expand All @@ -43,8 +46,19 @@ function createActorMapper(imageData) {
}

function createCT2dPipeline(imageData) {
const { actor, mapper } = createActorMapper(imageData)
mapper.setSampleDistance(5.0)
const { actor } = createActorMapper(imageData)
const cfun = vtkColorTransferFunction.newInstance()
/*
0: { description: 'Soft tissue', window: 400, level: 40 },
1: { description: 'Lung', window: 1500, level: -600 },
2: { description: 'Liver', window: 150, level: 90 },
3: { description: 'Bone', window: 2500, level: 480 },
4: { description: 'Brain', window: 80, level: 40 },*/
const preset = vtkColorMaps.getPresetByName('Grayscale')
cfun.applyColorMap(preset)
cfun.setMappingRange(-360, 440)

actor.getProperty().setRGBTransferFunction(0, cfun)

return actor
}
Expand All @@ -53,22 +67,18 @@ function createPET2dPipeline(imageData, petColorMapId) {
const { actor, mapper } = createActorMapper(imageData)
mapper.setSampleDistance(5.0)

const range = imageData
.getPointData()
.getScalars()
.getRange()

const cfun = vtkColorTransferFunction.newInstance()
const preset = vtkColorMaps.getPresetByName(petColorMapId)
cfun.applyColorMap(preset)
cfun.setMappingRange(range[0], (range[1] * 2) / 5)
cfun.setMappingRange(0, 5)

actor.getProperty().setRGBTransferFunction(0, cfun)

// Create scalar opacity function
const ofun = vtkPiecewiseFunction.newInstance()
ofun.addPoint(0.0, 0.0)
ofun.addPoint(range[1] / 4, 0.3)
ofun.addPoint(0, 0.0)
ofun.addPoint(0.1, 0.9);
ofun.addPoint(5, 1.0);

actor.getProperty().setScalarOpacity(0, ofun)

Expand Down Expand Up @@ -117,12 +127,6 @@ function applyPointsToRGBFunction(points, range, cfun) {
}

function applyPreset(actor, preset) {
/*const imageData = actor.getMapper().getInputData()
const dataRange = imageData
.getPointData()
.getScalars()
.getRange()*/

// Create color transfer function
const colorTransferArray = preset.colorTransfer
.split(' ')
Expand All @@ -134,7 +138,7 @@ function applyPreset(actor, preset) {
const width = shiftRange[1] - shiftRange[0];

// TODO: Something about the rescaling is still very wrong
const shift = -1000;//dataRange[0];
const shift = shiftRange[0];
min += shift;

const cfun = vtkColorTransferFunction.newInstance()
Expand All @@ -161,7 +165,7 @@ function applyPreset(actor, preset) {

const ofun = vtkPiecewiseFunction.newInstance()
const normPoints = [];
for (let i = 0; i < scalarOpacityArray.length; i+=2) {
for (let i = 0; i < scalarOpacityArray.length; i += 2) {
let value = scalarOpacityArray[i]
const opacity = scalarOpacityArray[i + 1]

Expand Down Expand Up @@ -227,7 +231,7 @@ function createCT3dPipeline(imageData, ctTransferFunctionPresetId) {

applyPreset(actor, preset)

actor.getProperty().setScalarOpacityUnitDistance(0, 4.5)
actor.getProperty().setScalarOpacityUnitDistance(0, 2.5)

return actor
}
Expand All @@ -246,22 +250,21 @@ function createPET3dPipeline(imageData, petColorMapId) {
mapper.setSampleDistance(sampleDistance);

// Apply colormap
const range = imageData
.getPointData()
.getScalars()
.getRange()
const cfun = vtkColorTransferFunction.newInstance()
cfun.applyColorMap(vtkColorMaps.getPresetByName(petColorMapId))
cfun.setMappingRange(range[0], (range[1] * 3) / 5)
const preset = vtkColorMaps.getPresetByName(petColorMapId)
cfun.applyColorMap(preset)
cfun.setMappingRange(0, 5)

actor.getProperty().setRGBTransferFunction(0, cfun)

// Create scalar opacity function
const ofun = vtkPiecewiseFunction.newInstance()
ofun.addPoint(0.0, 0.0)
ofun.addPoint(range[1] / 3, 0.2)
ofun.addPoint(0.1, 0.1)
ofun.addPoint(5, 0.2)

actor.getProperty().setScalarOpacity(0, ofun)
actor.getProperty().setScalarOpacityUnitDistance(0, 2.5)

return actor
}
Expand Down Expand Up @@ -321,12 +324,12 @@ class VTKFusionExample extends Component {
let ctImageIds = imageIds.filter(imageId =>
imageId.includes(ctSeriesInstanceUID)
)
ctImageIds = ctImageIds//.slice(0, 100)
//ctImageIds = ctImageIds.slice(0, ctImageIds.length / 4)

let petImageIds = imageIds.filter(imageId =>
imageId.includes(petSeriesInstanceUID)
)
petImageIds = petImageIds.slice(0, 100)
petImageIds = petImageIds.slice(0, petImageIds.length / 4)

const ctImageDataPromise = loadDataset(ctImageIds, 'ctDisplaySet')
const petImageDataPromise = loadDataset(petImageIds, 'petDisplaySet')
Expand Down Expand Up @@ -378,19 +381,29 @@ class VTKFusionExample extends Component {
const actor2d = this.state.volumes[1]
const actor3d = this.state.volumeRenderingVolumes[1]

const imageData = actor2d.getMapper().getInputData()
const range = imageData
.getPointData()
.getScalars()
.getRange()

const preset = vtkColorMaps
.getPresetByName(petColorMapId);

[(actor2d, actor3d)].forEach(actor => {
[actor2d, actor3d].forEach(actor => {
if (!actor) {
return;
}

const cfun = actor.getProperty().getRGBTransferFunction(0)

// TODO: Looks like this is returned by reference and mutated when
// applyColorMap is run, so we are copying the array with .slice().
// - Bit surprised we have to do this though. I wonder where else this is
// causing issues
const cRange = cfun.getMappingRange().slice();
cfun.applyColorMap(preset)
cfun.setMappingRange(range[0], (range[1] * 2) / 5)

const newCfun = vtkColorTransferFunction.newInstance()
newCfun.applyColorMap(preset);
newCfun.setMappingRange(cRange[0], cRange[1])

// TODO: Why doesn't mutating the current RGBTransferFunction work?
actor.getProperty().setRGBTransferFunction(0, newCfun);
})

this.setState({
Expand Down
30 changes: 14 additions & 16 deletions example/src/initCornerstone.js
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Original file line number Diff line number Diff line change
Expand Up @@ -28,22 +28,20 @@ cornerstoneTools.toolColors.setActiveColor('rgb(0, 255, 0)');

cornerstoneTools.store.state.touchProximity = 40;

const config = {
maxWebWorkers: 4,//Math.max(navigator.hardwareConcurrency - 1, 1),
startWebWorkersOnDemand: true,
webWorkerPath: '/cornerstoneWADOImageLoaderWebWorker.min.js',
taskConfiguration: {
decodeTask: {
loadCodecsOnStartup: true,
initializeCodecsOnStartup: false,
codecsPath: '/cornerstoneWADOImageLoaderCodecs.min.js',
usePDFJS: false,
strict: false
}
}
};

cornerstoneWADOImageLoader.webWorkerManager.initialize(config);
window.cornerstone = cornerstone;

cornerstoneWADOImageLoader.external.cornerstone = cornerstone;
cornerstoneWADOImageLoader.external.dicomParser = dicomParser;

var config = {
maxWebWorkers: navigator.hardwareConcurrency || 1,
startWebWorkersOnDemand : true,
taskConfiguration: {
decodeTask: {
initializeCodecsOnStartup: false,
usePDFJS: false,
strict: false,
},
}
};
cornerstoneWADOImageLoader.webWorkerManager.initialize(config);
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